China Scholarship Council: Breaking the barrier: Improving antibiotic design by machine learning


   School of Life Sciences

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  Prof U Zachariae, Dr R Sknepnek  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Antibiotic resistance is a global health problem of increasing severity. Infections caused by Gram-negative bacteria are especially difficult to treat owing to the poor permeability of their cell envelope and the efficiency of multidrug efflux pumps, which prevents drugs from accumulating near their targets. Overcoming the permeability barrier in Gram-negative bacteria is therefore a biomedical problem of great importance, which however so far remains unsolved.  

In this project, we will use a combination of machine-learning, molecular modelling, and biomolecular simulations to identify molecules or molecular features that enhance drug accumulation within the cells of Gram-negative bacteria, and at the same time avoid or block efflux pumps. The structures and structural models of efflux pumps will be employed to screen compound libraries for potential inhibitors and avoiders, and the simulations will then allow you to obtain a mechanistic understanding of these interactions. Making use of large datasets from experimental databases, you will then construct machine learning models to predict structures that can serve as good permeators and efflux inhibitors. The project will focus on the Gram-negative pathogens Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. 

The results of this project will inform medicinal chemists about novel strategies to develop improved broad-spectrum antibiotics.   

Biological Sciences (4) Chemistry (6) Computer Science (8)

Funding Notes

In order to be eligible for these awards applicants must:
Be a Chinese national
Meet the requirements of the CSC – please see their website
Hold an unconditional offer to study for a PhD at the University of Dundee and meet our English language requirements
Have completed a bachelors or masters degree before the agreed start of PhD study.
Already have an IELTS score of 6.5 at time of applying
For further information on the CSC programme please visit https://www.dundee.ac.uk/phds/funding/china-scholarship-council-csc-programme and apply by completing our application form - https://dundee.onlinesurveys.ac.uk/csc-programme-2024-entry

References

References:
Gurvic, Leach & Zachariae, J. Med. Chem. 65, 6088-6099 (2022).
Gurvic & Zachariae, bioRxiv, 2023.07.13.548850 (2023).
Maher & Hassan, mBio, doi: 10.1128/mbio.01205-23 (2023).

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